Non-synonymous FGD3 Variant as Positional Candidate for Disproportional Tall Stature Accounting for a Carcass Weight QTL (CW-3) and Skeletal Dysplasia in Japanese Black Cattle

Presence of a Deletion Mutation of Myostatin (MSTN) Gene Associated With Double-Muscling Phenotype in Japanese Black Cattle Population

Mutations in the bovine myostatin (MSTN) gene have been identified as the causative factor for the double-muscling phenotype in several European cattle breeds, including Belgian Blue, Piedmontese, and Shorthorn. In Japan, following the Meiji Restoration, several European breeds, including Shorthorn, Brown Swiss, Devon, Simmental, and Ayrshire, were introduced and crossbred with native cattle to develop modern Japanese beef cattle breeds, such as Japanese Black cattle. Historical records regarding the breeding of Japanese Black cattle indicate that the double-muscling phenotype, referred to as "Butajiri," occasionally appeared in Japanese Black cattle population. These historical observations suggest the potential presence of MSTN gene mutation in the Japanese Black cattle population. The aim of this study was, therefore, to investigate the presence of MSTN gene mutation in the current Japanese Black cattle population. Through screening 400 reproductive females, we identified one cow carrying an 11-bp deletion in the MSTN gene. While further investigation of the animals in the pedigree of this cow could not reveal any living animals with this mutation, this is the first report demonstrating the presence of the MSTN mutation in the Japanese Black cattle population.

Unlocking the Transcriptional Control of NCAPG in Bovine Myoblasts: CREB1 and MYOD1 as Key Players

Muscle formation directly determines meat production and quality. The non-SMC condensin I complex subunit G (NCAPG) is strongly linked to the growth features of domestic animals because it is essential in controlling muscle growth and development. This study aims to elucidate the tissue expression level of the bovine NCAPG gene, and determine the key transcription factors for regulating the bovine NCAPG gene. In this study, we observed that the bovine NCAPG gene exhibited high expression levels in longissimus dorsi and spleen tissues. Subsequently, we cloned and characterized the promoter region of the bovine NCAPG gene, consisting of a 2039 bp sequence, through constructing the deletion fragment double-luciferase reporter vector and site-directed mutation-identifying core promoter region with its key transcription factor binding site. In addition, the key transcription factors of the core promoter sequence of the bovine NCAPG gene were analyzed and predicted using online software. Furthermore, by integrating overexpression experiments and the electrophoretic mobility shift assay (EMSA), we have shown that cAMP response element binding protein 1 (CREB1) and myogenic differentiation 1 (MYOD1) bind to the core promoter region (-598/+87), activating transcription activity in the bovine NCAPG gene. In conclusion, these findings shed important light on the regulatory network mechanism that underlies the expression of the NCAPG gene throughout the development of the muscles in beef cattle.

The growth curve determination and economic trait correlation for Qinchuan bull population

Carcass weight, as a measure of meat yield, and body measurements are directly correlated traits in livestock. However, longitudinally collected phenotype records of local breeds are not comprehensive. The research was performed on Qinchuan bull population to understand their growth and development, and data from Qinchuan bull that was weighed and measured at birth, 6, 12, 18, and 24 months of age was analyzed. Furthermore, Logistic, Brody, Gompertz, and Bertallanffy were used to fit the growth curves for weight and body size traits. The results showed that the four curve models have good fitting degrees for the weight and body size (R2 > 0.99), and the Bertallanffy model exhibited a good fit to the measured data of body weight, and the model estimated the inflection point of body weight as (5.43 months of age, 122.01 kg). Particularly, the limited mature body weight can reach 557.8 kg by the Brody model. Body weight was significantly positively correlated with body height, hip height, body length, chest circumference, abdominal girth, and calf girth (p < 0.0001), and the correlation between body weight and body length was the highest (r = 0.975). The regression equation predicting body weight was Y = -275.691 + 3.28 X3 + 1.311 X4 - 0.397 X5.

Fitting Genomic Prediction Models with Different Marker Effects among Prefectures to Carcass Traits in Japanese Black Cattle

We fitted statistical models, which assumed single-nucleotide polymorphism (SNP) marker effects differing across the fattened steers marketed into different prefectures, to the records for cold carcass weight (CW) and marbling score (MS) of 1036, 733, and 279 Japanese Black fattened steers marketed into Tottori, Hiroshima, and Hyogo prefectures in Japan, respectively. Genotype data on 33,059 SNPs was used. Five models that assume only common SNP effects to all the steers (model 1), common effects plus SNP effects differing between the steers marketed into Hyogo prefecture and others (model 2), only the SNP effects differing between Hyogo steers and others (model 3), common effects plus SNP effects specific to each prefecture (model 4), and only the effects specific to each prefecture (model 5) were exploited. For both traits, slightly lower values of residual variance than that of model 1 were estimated when fitting all other models. Estimated genetic correlation among the prefectures in models 2 and 4 ranged to 0.53 to 0.71, all <0.8. These results might support that the SNP effects differ among the prefectures to some degree, although we discussed the necessity of careful consideration to interpret the current results.

Computational Analysis of the Immune Infiltration Pattern and Candidate Diagnostic Biomarkers in Lumbar Disc Herniation

Objectives

Lumbar disc herniation (LDH) is a musculoskeletal disease that contributes to low back pain, sciatica, and movement disorder. Existing studies have suggested that the immune environment factors are the primary contributions to LDH. However, its etiology remains unknown. We sought to identify the potential diagnostic biomarkers and analyze the immune infiltration pattern in LDH.

Methods

The whole-blood gene expression level profiles of GSE124272 and GSE150408 were downloaded from the Gene Expression Omnibus (GEO) database, including that of 25 patients with LDH and 25 healthy volunteers. After merging the two microarray datasets, Differentially Expressed Genes (DEGs) were screened, and a functional correlation analysis was performed. The Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression algorithm and support vector machine recursive feature elimination (SVM-RFE) were applied to identify diagnostic biomarkers by a cross-validation method. Then, the GSE42611 dataset was used as a validation dataset to detect the expression level of these diagnostic biomarkers in the nucleus pulposus and evaluate their accuracy. The hub genes in the network were identified by the CIBERSORT tool and the Weighted Gene Coexpression Network Analysis (WGCNA). A Spearman correlation analysis between diagnostic markers and infiltrating immune cells was conducted to further illustrate the molecular immune mechanism of LDH.

Results

The azurophil granule and the systemic lupus erythematosus pathway were significantly different between the healthy group and the LDH group after gene enrichment analysis. The XLOC_l2_012836, lnc-FGD3-1, and scavenger receptor class A member 5 were correlated with the immune cell infiltration in various degrees. In addition, five hub genes that correlated with LDH were identified, including AQP9, SIRPB2, SLC16A3, LILRB3, and HSPA6.

Conclusion

The XLOC_l2_012836, lnc-FGD3-1, and SCARA5 might be adopted for the early diagnosis of LDH. The five identified hub genes might have similar pathological mechanisms that contribute to the degeneration of the lumbar disc. The identified hub genes and immune infiltrating pattern extend the knowledge on the potential functioning mechanisms, which offer guidance for the development of therapeutic targets of LDH.

Cross-population selection signatures in Canchim composite beef cattle

Analyses of livestock genomes have been used to detect selection signatures, which are genomic regions associated with traits under selection leading to a change in allele frequency. The objective of the present study was to characterize selection signatures in Canchim composite beef cattle using cross-population analyses with the founder Nelore and Charolais breeds. High-density single nucleotide polymorphism genotypes were available on 395 Canchim representing the target population, along with genotypes from 809 Nelore and 897 Charolais animals representing the reference populations. Most of the selection signatures were co-located with genes whose functions agree with the expectations of the breeding programs; these genes have previously been reported to associate with meat quality, as well as reproductive traits. Identified genes were related to immunity, adaptation, morphology, as well as behavior, could give new perspectives for understanding the genetic architecture of Canchim. Some selection signatures identified genes that were recently introduced in Canchim, such as the loci related to the polled trait.

Estimation of the autosomal contribution to total additive genetic variability of carcass traits in Japanese Black cattle

We attempted to estimate the additive genetic variance explained by each autosome, using genotype data of 33,657 single nucleotide polymorphism (SNP) markers in 2271 Japanese Black fattened steers. Traits were cold carcass weight, ribeye area, rib thickness, subcutaneous fat thickness, estimated yield percentage, and marbling score. Two mixed linear models were used: One is that (model 1) incorporating a genomic relationship matrix (G matrix) constructed by using all available SNPs, and another (model 2), incorporating two G matrices constructed by using the SNPs on one autosome and using those on the remaining autosomes. Genomic heritabilities estimated using model 1 were moderate to high. The sums of the proportions of the additive genetic variance explained by each autosome to the total genetic variance estimated by using model 2 were >90%. For carcass weight, the proportions explained by Bos taurus autosomes 6, 8, and 14 were higher than those explained by the remaining autosomes. In some cases, the estimated proportion was close to 0. The results obtained from model 2 could provide a novel insight into the genetic architecture, such as heritability per chromosome, of carcass traits in Japanese Black cattle, although further careful investigation would be required.

Genotyping and Whole-Genome Resequencing of Welsh Sheep Breeds Reveal Candidate Genes and Variants for Adaptation to Local Environment and Socioeconomic Traits

Background

Advances in genetic tools applied to livestock breeding has prompted research into the previously neglected breeds adapted to harsh local environments. One such group is the Welsh mountain sheep breeds, which can be farmed at altitudes of 300 m above sea level but are considered to have a low productive value because of their poor wool quality and small carcass size. This is contrary to the lowland breeds which are more suited to wool and meat production qualities, but do not fare well on upland pasture. Herein, medium-density genotyping data from 317 individuals representing 15 Welsh sheep breeds were used alongside the whole-genome resequencing data of 14 breeds from the same set to scan for the signatures of selection and candidate genetic variants using haplotype- and SNP-based approaches.

Results

Haplotype-based selection scan performed on the genotyping data pointed to a strong selection in the regions of GBA3, PPARGC1A, APOB, and PPP1R16B genes in the upland breeds, and RNF24, PANK2, and MUC15 in the lowland breeds. SNP-based selection scan performed on the resequencing data pointed to the missense mutations under putative selection relating to a local adaptation in the upland breeds with functions such as angiogenesis (VASH1), anti-oxidation (RWDD1), cell stress (HSPA5), membrane transport (ABCA13 and SLC22A7), and insulin signaling (PTPN1 and GIGFY1). By contrast, genes containing candidate missense mutations in the lowland breeds are related to cell cycle (CDK5RAP2), cell adhesion (CDHR3), and coat color (MC1R).

Conclusion

We found new variants in genes with potentially functional consequences to the adaptation of local sheep to their environments in Wales. Knowledge of these variations is important for improving the adaptative qualities of UK and world sheep breeds through a marker-assisted selection.

Identification of Major Loci and Candidate Genes for Meat Production-Related Traits in Broilers

Background

Carcass traits are crucial characteristics of broilers. However, the underlying genetic mechanisms are not well understood. In the current study, significant loci and major-effect candidate genes affecting nine carcass traits related to meat production were analyzed in 873 purebred broilers using an imputation-based genome-wide association study.

Results

The heritability estimates of nine carcass traits, including carcass weight, thigh muscle weight, and thigh muscle percentage, were moderate to high and ranged from 0.21 to 0.39. Twelve genome-wide significant SNPs and 118 suggestively significant SNPs of 546,656 autosomal variants were associated with carcass traits. All SNPs for six weight traits (body weight at 42 days of age, carcass weight, eviscerated weight, whole thigh weight, thigh weight, and thigh muscle weight) were clustered around the 24.08 Kb region (GGA24: 5.73–5.75 Mb) and contained only one candidate gene (DRD2). The most significant SNP, rs15226023, accounted for 4.85–7.71% of the estimated genetic variance of the six weight traits. The remaining SNPs for carcass composition traits (whole thigh percentage and thigh percentage) were clustered around the 42.52 Kb region (GGA3: 53.03–53.08 Mb) and contained only one candidate gene (ADGRG6). The most significant SNP in this region, rs13571431, accounted for 11.89–13.56% of the estimated genetic variance of two carcass composition traits. Some degree of genetic differentiation in ADGRG6 between large and small breeds was observed.

Conclusion

We identified one 24.08 Kb region for weight traits and one 42.52 Kb region for thigh-related carcass traits. DRD2 was the major-effect candidate gene for weight traits, and ADGRG6 was the major-effect candidate gene for carcass composition traits. Our results supply essential information for causative mutation identification of carcass traits in broilers.

Identification of deleterious recessive haplotypes and candidate deleterious recessive mutations in Japanese Black cattle

Intensive use of a few elite sires has increased the risk of the manifestation of deleterious recessive traits in cattle. Substantial genotyping data gathered using single-nucleotide polymorphism (SNP) arrays have identified the haplotypes with homozygous deficiency, which may compromise survival. We developed Japanese Black cattle haplotypes (JBHs) using SNP array data (4843 individuals) and identified deleterious recessive haplotypes using exome sequencing of 517 sires. We identified seven JBHs with homozygous deficiency. JBH_10 and JBH_17 were associated with the resuming of estrus after artificial insemination, indicating that these haplotypes carried deleterious mutations affecting embryonic survival. The exome data of 517 Japanese Black sires revealed that AC_000165.1:g.85341291C>G of IARS in JBH_8_2, AC_000174.1:g.74743512G>T of CDC45 in JBH_17, and a copy variation region (CNVR_27) of CLDN16 in JBH_1_1 and JBH_1_2 were the candidate mutations. A novel variant AC_000174.1:g.74743512G>T of CDC45 in JBH_17 was located in a splicing donor site at a distance of 5 bp, affecting pre-mRNA splicing. Mating between heterozygotes of JBH_17 indicated that homozygotes carrying the risk allele died around the blastocyst stage. Analysis of frequency of the CDC45 risk allele revealed that its carriers were widespread throughout the tested Japanese Black cattle population. Our approach can effectively manage the inheritance of recessive risk alleles in a breeding population.

A genome-wide association study reveals a quantitative trait locus for calf mortality on chromosome 9 in Japanese Black cattle

Calf mortality is a major problem affecting cattle production. To identify genetic variants associated with calf mortality in Japanese Black cattle, we evaluated calf mortality as a categorical trait using a threshold model and conducted a GWAS. We identified two SNPs between 32 549 297 and 32 606 924 bp on bovine chromosome 9 that were significantly associated with calf mortality from 61 to 180 days after birth. The SNP showing the highest association was localized at a region 624 bp downstream of exon 4 of the anti-silencing function 1A histone chaperone gene (ASF1A) that promotes DNA damage repair, and the null mice, which exhibit pre- and postnatal lethality. This association was also detected using the breeding value of 334 sires. The frequency of the risk allele in Japanese Black cattle from locations across Japan was 0.013; although the frequency of ASF1A risk allele was low, it is widespread in the Japanese Black cattle population. Thus, it may be necessary to routinely monitor the cattle population for the presence of this allele.

A long-term study of the effects of SLC12A1 homozygous mutation (g.62382825G>A, p.Pro372Leu) in Japanese Black cattle

Recessive missense mutation in the solute carrier family 12, member 1 (SLC12A1) gene (g.62382825G>A) is associated with hydrallantois, which is the accumulation of fluid in the allantoic cavity of a pregnant animal, and usually causes fetal death in Japanese Black cattle. However, the symptoms of a homozygote with this mutation that do not result in fetal death have not previously been tracked and evaluated. In the present study, we observed a homozygote with the SLC12A1 risk allele over a long-term period. The calf did not show any obvious clinical symptoms, although it did exhibit a slight growth retardation that accompanied mild calciuria. At 28 months of age, the homozygote showed renal dysfunction, which in turn resulted in hydronephrosis. The time course of the symptoms was consistent with the phenotype of Bartter syndrome in humans. Additionally, the risk heterozygous genotype did not any effects on carcass traits, which indicates that eliminating the risk allele would not have any unfavorable effects. Therefore, we emphasize that both the fetal- and late-stage symptoms associated with the SLC12A1 risk allele compromise animal welfare, and consequently may result in severe economic losses for individual farmers if the SLC12A1 risk allele is not eliminated from the population.

Genetic and genomic analyses for predicted methane-related traits in Japanese Black steers

The objectives of this study were to estimate genetic parameters and to perform a genome‐wide association study (GWAS) for predicted methane‐related traits in Japanese Black steers. The methane production and yield traits were predicted using on‐farm measurable traits, such as dry matter intake and average daily gain. A total of 4,578 Japanese Black steers, which were progenies of 362 sires genotyped with imputed 551,995 single nucleotide polymorphisms (SNPs), had phenotypes of predicted methane‐related traits during the total fattening period (52 weeks). For the estimation of genetic parameters, the estimated heritabilities were moderate (ranged from 0.57 to 0.60). In addition, the estimated genetic correlations of methane production traits with most of carcass traits and feed‐efficiency traits were unfavorable, but those of methane yield traits were favorable or low. For the GWAS, no genome‐wide significant SNP was detected, but a total of four quantitative trait locus (QTL) regions that explained more than 5.0% of genetic variance were localized on the genome, and some candidate genes associated with growth and feed‐efficiency traits were located on the regions. Our results suggest that the predicted methane‐related traits are heritable and some QTL regions for the traits are localized on the genome in Japanese Black steers.

Genome-wide association study and genomic evaluation of feed efficiency traits in Japanese Black cattle using single-step genomic best linear unbiased prediction method

The objectives of this study were to better understand the genetic architecture and the possibility of genomic evaluation for feed efficiency traits by (i) performing genome-wide association studies (GWAS), and (ii) assessing the accuracy of genomic evaluation for feed efficiency traits, using single-step genomic best linear unbiased prediction (ssGBLUP)-based methods. The analyses were performed in residual feed intake (RFI), residual body weight gain (RG), and residual intake and body weight gain (RIG) during three different fattening periods. The phenotypes from 4,578 Japanese Black steers, which were progenies of 362 progeny-tested bulls and the genotypes from the bulls were used in this study. The results of GWAS showed that a total of 16, 8, and 12 gene ontology terms were related to RFI, RG, and RIG, respectively, and the candidate genes identified in RFI and RG were involved in olfactory transduction and the phosphatidylinositol signaling system, respectively. The realized reliabilities of genomic estimated breeding values were low to moderate in the feed efficiency traits. In conclusion, ssGBLUP-based method can lead to understand some biological functions related to feed efficiency traits, even with small population with genotypes, however, an alternative strategy will be needed to enhance the reliability of genomic evaluation.

Genomic analyses suggest adaptive differentiation of northern European native cattle breeds

Native domestic breeds represent important cultural heritage and genetic diversity relevant for production traits, environmental adaptation and food security. However, risks associated with low effective population size, such as inbreeding and genetic drift, have elevated concerns over whether unique within-breed lineages should be kept separate or managed as one population. As a conservation genomic case study of the genetic diversity represented by native breeds, we examined native and commercial cattle (Bos taurus) breeds including the threatened Danish Jutland cattle. We examined population structure and genetic diversity within breeds and lineages genotyped across 770K single nucleotide polymorphism loci to determine (a) the amount and distribution of genetic diversity in native breeds, and (b) the role of genetic drift versus selection. We further investigated the presence of outlier loci to detect (c) signatures of environmental selection in native versus commercial breeds, and (d) native breed adaptation to various landscapes. Moreover, we included older cryopreserved samples to determine (e) whether cryopreservation allows (re)introduction of original genetic diversity. We investigated a final set of 195 individuals and 677K autosomal loci for genetic diversity within and among breeds, examined population structure with principal component analyses and a maximum-likelihood approach and searched for outlier loci suggesting artificial or natural selection. Our findings demonstrate the potential of genomics for identifying the uniqueness of native domestic breeds, and for maintaining their genetic diversity and long-term evolutionary potential through conservation plans balancing inbreeding with carefully designed outcrossing. One promising opportunity is the use of cryopreserved samples, which can provide important genetic diversity for populations with few individuals, while helping to preserve their traditional genetic characteristics. Outlier tests for native versus commercial breeds identified genes associated with climate adaptation, immunity and metabolism, and native breeds may carry genetic variation important for animal health and robustness in a changing climate.

Effect of two non-synonymous ecto-5'-nucleotidase variants on the genetic architecture of inosine 5'-monophosphate (IMP) and its degradation products in Japanese Black beef

Background

Umami is a Japanese term for the fifth basic taste and is an important sensory property of beef palatability. Inosine 5′-monophosphate (IMP) contributes to umami taste in beef. Thus, the overall change in concentration of IMP and its degradation products can potentially affect the beef palatability. In this study, we investigated the genetic architecture of IMP and its degradation products in Japanese Black beef. First, we performed genome-wide association study (GWAS), candidate gene analysis, and functional analysis to detect the causal variants that affect IMP, inosine, and hypoxanthine. Second, we evaluated the allele frequencies in the different breeds, the contribution of genetic variance, and the effect on other economical traits using the detected variants.

Results

A total of 574 Japanese Black cattle were genotyped using the Illumina BovineSNP50 BeadChip and were then used for GWAS. The results of GWAS showed that the genome-wide significant single nucleotide polymorphisms (SNPs) on BTA9 were detected for IMP, inosine, and hypoxanthine. The ecto-5′-nucleotidase (NT5E) gene, which encodes the enzyme NT5E for the extracellular degradation of IMP to inosine, was located near the significant region on BTA9. The results of candidate gene analysis and functional analysis showed that two non-synonymous SNPs (c.1318C > T and c.1475 T > A) in NT5E affected the amount of IMP and its degradation products in beef by regulating the enzymatic activity of NT5E. The Q haplotype showed a positive effect on IMP and a negative effect on the enzymatic activity of NT5E in IMP degradation. The two SNPs were under perfect linkage disequilibrium in five different breeds, and different haplotype frequencies were seen among breeds. The two SNPs contribute to about half of the total genetic variance in IMP, and the results of genetic relationship between IMP and its degradation products showed that NT5E affected the overall concentration balance of IMP and its degradation products. In addition, the SNPs in NT5E did not have an unfavorable effect on the other economical traits.

Conclusion

Based on all the above findings taken together, two non-synonymous SNPs in NT5E would be useful for improving IMP and its degradation products by marker-assisted selection in Japanese Black cattle.

Electronic supplementary material

The online version of this article (doi: 10.1186/s12864-017-4275-4) contains supplementary material, which is available to authorized users.

Critical Roles of Dual-Specificity Phosphatases in Neuronal Proteostasis and Neurological Diseases

Protein homeostasis or proteostasis is a fundamental cellular property that encompasses the dynamic balancing of processes in the proteostasis network (PN). Such processes include protein synthesis, folding, and degradation in both non-stressed and stressful conditions. The role of the PN in neurodegenerative disease is well-documented, where it is known to respond to changes in protein folding states or toxic gain-of-function protein aggregation. Dual-specificity phosphatases have recently emerged as important participants in maintaining balance within the PN, acting through modulation of cellular signaling pathways that are involved in neurodegeneration. In this review, we will summarize recent findings describing the roles of dual-specificity phosphatases in neurodegeneration and offer perspectives on future therapeutic directions.

Genetic Variants in SDC3 Gene are Significantly Associated with Growth Traits in Two Chinese Beef Cattle Breeds

Identification of the genes and polymorphisms underlying quantitative traits, and understanding these genes and polymorphisms affect economic growth traits, are important for successful marker-assisted selection and more efficient management strategies in commercial cattle (Bos taurus) population. Syndecan-3 (SDC3), a member of the syndecan family of type I transmembrane heparan sulfate proteoglycans is a novel regulator of feeding behavior and body weight. The aim of this study is to examine the association of the SDC3 polymorphism with growth traits in Chinese Jiaxian and Qinchuan cattle breeds (). Four single nucleotide polymorphisms (SNPs: 1-4) were detected in 555 cows from three Chinese native cattle breeds by means of sequencing pooled DNA samples and polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) methods. We found one SNP (g.28362A > G) in intron and three SNPs (g.30742T > G, g.30821C > T and 33418 A > G) in exons. The statistical analyses indicated that these SNPs of SDC3 gene were associated with bovine body height, body length, chest circumference, and circumference of cannon bone (P < 0.05). The mutant-type variant was superior for growth traits; the heterozygote was associated with higher growth traits compared to wild-type homozygote. Our result confirms the polymorphisms in the SDC3 gene are associated with growth traits that may be used for marker-assisted selection in beef cattle breeding programs.

Loss of maternal ANNEXIN A10 via a 34-kb deleted-type copy number variation is associated with embryonic mortality in Japanese Black cattle

Background

Conception is a fundamental trait for successful cattle reproduction. However, conception rates in Japanese Black cattle have been gradually declining over the last two decades. Although conception failures are mainly caused by embryonic mortality, the role of maternal genetic factors in the process remains unknown. Copy number variation (CNV), defined as large-scale genomic structural variants, contributes to several genetic disorders. To identify CNV associated with embryonic mortality in Japanese Black cattle, we evaluated embryonic mortality as a categorical trait with a threshold model and conducted a genome-wide CNV association study for embryonic mortality using 791 animals.

Results

We identified a deleted-type CNV ranging from 378,127 to 412,061 bp on bovine chromosome 8, which was associated with embryonic mortality at 30–60 days after artificial insemination (AI). The CNV harbors exon 2 to 6 of ANNEXIN A10 (ANXA10). Analysis of sequence traces from the CNV identified that 63 bp reads bridging the breakpoint were present on both sides of the CNV, indicating that the CNV was generated by non-allelic homologous recombination using the 63 bp homologous sequences. Western blot analysis showed that the CNV results in a null allele of ANXA10. This association was replicated using a sample population size of 2552 animals. To elucidate the function of ANXA10 in vivo, we generated Anxa10 null mice using the CRISPR/Cas9 system. Crossbreeding experiments showed that litter size from crosses of both Anxa10^-/- and Anxa10^+/- females had fewer pups than did Anxa10^+/+ females, and embryos of Anxa10^-/- females died between implantation stages E4.5 and E12.5. These results indicate that loss of maternal Anxa10 causes embryonic mortality.

Conclusions

This study identified a deleted-type CNV encompassing ANXA10 in cows that was associated with embryonic mortality at 30–60 days after AI. Using a mouse model, we confirmed that litter sizes were smaller in crosses of both Anxa10^-/- and Anxa10^+/- females relative to those of wild females. These results indicate that ANXA10 is a maternal factor that is critical for embryo development.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3312-z) contains supplementary material, which is available to authorized users.

Genome-wide association study for carcass traits, fatty acid composition, chemical composition, sugar, and the effects of related candidate genes in Japanese Black cattle

We performed a genome-wide association study (GWAS) and candidate gene analysis to: (i) evaluate the effectiveness of the GWAS in our small population by performing GWAS for carcass weight (CW) and fatty acid composition; (ii) detect novel candidate regions affecting non-CW carcass traits, chemical composition and sugar; and (iii) evaluate the association of the candidate genes previously detected in CW and fatty acid composition with other economically important traits. A total of 574 Japanese Black cattle and 40 657 Single nucleotide polymorphisms were used. In addition, candidate gene analyses were performed to evaluate the association of three CW-related genes and two fatty acid-related genes with carcass traits, fatty acid composition, chemical composition and sugar. The significant regions with the candidate genes were detected for CW and fatty acid composition, and these results showed that a significant region would be detectable despite the small sample size. The novel candidate regions were detected on BTA23 for crude protein and on BTA19 for fructose. CW-related genes associated with the rib-eye area and fatty acid composition were identified, and fatty acid-related genes had no relationship with other traits. Moreover, the favorable allele of CW-related genes had an unfavorable effect on fatty acid composition.